Updated: Wed May 31 01:52:16 2017
RPKM of DNA methylation regulators

CpG coverage profile
- TCGA data have particularly lower coverage.

Global hypermethylation in IDH mut glioma
- Genome-wide and CGI hypermethylation in IDH mutant glioma samples: CEMT19, CEMT22, and CEMT_47.
- CEMT_21 (10% IDH mutation frequency) showed methylation levels closer to IDH wildtype samples.
- TCGA data seem to have lower fractional methylation geonme-wide, possibly due to different processing pipeline.
- Whiskers of the box plot represent 10% and 90% quantile.

DNA methylation changes around CGI edges
- CGIs are hypermethylated in IDH mutant gliomas.
- DNA methylation changes around CGI occur at the edge of CGIs.
DMRs between gliomas and NPCs
DMR identification
- Identify DM CpGs
- CpG coverage in both samples \(\ge\) 3;
- methyl_diff one-sided p-value \(\le\) 0.0005;
- delta fractional methylation \(\ge\) 0.6;
- fractional methylation of one sample \(\ge\) 0.75.
- Collapse DM CpGs into DMRs
- adjacent DM CpGs have the same DM status;
- distance between adjacent CpGs (size) \(\le\) 500bp;
- No. of CpGs within each DMR \(\ge\) 3.
Total DMR length
- Hypermethylation in IDH mut samples.
- Hypomethylation in IDH wt glioma: CEMT_23 (GBM).
- CEMT_21 had the least amount of DMRs and no bias towards hyper or hypo.
- Results against different NPCs were reasonably similar (intersect statistically significant).

DMR GREAT analysis
- DMR - gene association
- Proximal: 5kb upstream, 1kb downstream.
- Distal: up to 20kb.
Percentage of hyper CpGs in hyper CGIs

Methylated CGIs associated with transcription
|
Sample
|
CGI
|
CGI_hyper
|
CGI_K36
|
CGI_hyper_K36
|
p
|
|
CEMT_19
|
5066
|
1685
|
290
|
216
|
0
|
|
CEMT_21
|
5066
|
1085
|
126
|
91
|
0
|
|
CEMT_22
|
5066
|
1739
|
328
|
227
|
0
|
|
CEMT_23
|
5066
|
1015
|
218
|
103
|
0
|
|
CEMT_47
|
5066
|
1724
|
165
|
138
|
0
|
Hypermethylated CGIs associated with transcription
- There are on average 15% of hypermethylated CGIs overlapping with H3K36me3 enriched regions, 8% of them are not in genebody in IDH mut gliomas, suggesting possible enhancer RNA expression.
|
Sample
|
hyper
|
CGI
|
Non.gene_CGI
|
H3K36me3
|
Non.gene
|
p_Fisher
|
|
CEMT_19
|
19105
|
6042
|
1197
|
946
|
72
|
1.0000000
|
|
CEMT_21
|
1793
|
313
|
50
|
61
|
5
|
0.9568727
|
|
CEMT_22
|
17291
|
4733
|
919
|
843
|
64
|
1.0000000
|
|
CEMT_23
|
1718
|
703
|
107
|
162
|
5
|
1.0000000
|
|
CEMT_47
|
22146
|
6034
|
1222
|
629
|
36
|
1.0000000
|
DMR enrichment in genomic regions
- Enriched in CGIs and CGI shores, esp. hypermethylation in CGIs.
- Promoter: TSS +/- 2kb; CGI_shore: CGI +/- 2kb.

DMR enrichment in chromatin states
- Hypermethylated regions were enriched in H3K27me3 marked chromatin states.
- Hypomethylated regions were enriched in enhancer regions.

DMR intersect with differentially marked histone modifications
